7KLG

SARS-CoV-2 RBD in complex with Fab 15033

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.272 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations.

Miersch, S., Li, Z., Saberianfar, R., Ustav, M., Brett Case, J., Blazer, L., Chen, C., Ye, W., Pavlenco, A., Gorelik, M., Garcia Perez, J., Subramania, S., Singh, S., Ploder, L., Ganaie, S., Chen, R.E., Leung, D.W., Pandolfi, P.P., Novelli, G., Matusali, G., Colavita, F., Capobianchi, M.R., Jain, S., Gupta, J.B., Amarasinghe, G.K., Diamond, M.S., Rini, J., Sidhu, S.S.

(2021) J Mol Biol 433: 167177-167177

  • DOI: https://doi.org/10.1016/j.jmb.2021.167177
  • Primary Citation of Related Structures:  
    7KLG, 7KLH, 7KMK, 7KML, 7KXJ, 7KXK

  • PubMed Abstract: 

    • Neutralizing antibodies (nAbs) hold promise as therapeutics against COVID-19. Here, we describe protein engineering and modular design principles that have led to the development of synthetic bivalent and tetravalent nAbs against SARS-CoV-2. The best nAb targets the host receptor binding site of the viral S-protein and tetravalent versions block entry with a potency exceeding bivalent nAbs by an order of magnitude ...

    Neutralizing antibodies (nAbs) hold promise as therapeutics against COVID-19. Here, we describe protein engineering and modular design principles that have led to the development of synthetic bivalent and tetravalent nAbs against SARS-CoV-2. The best nAb targets the host receptor binding site of the viral S-protein and tetravalent versions block entry with a potency exceeding bivalent nAbs by an order of magnitude. Structural studies show that both the bivalent and tetravalent nAbs can make multivalent interactions with a single S-protein trimer, consistent with the avidity and potency of these molecules. Significantly, we show that the tetravalent nAbs show increased tolerance to potential virus escape mutants and an emerging variant of concern. Bivalent and tetravalent nAbs can be produced at large-scale and are as stable and specific as approved antibody drugs. Our results provide a general framework for enhancing antiviral therapies against COVID-19 and related viral threats, and our strategy can be applied to virtually any antibody drug.

    Related Citations: 
    • Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations.
      Miersch, S., Li, Z., Saberianfar, R., Ustav, M., Case, J.B., Blazer, L., Chen, C., Ye, W., Pavlenco, A., Gorelik, M., Perez, J.G., Subramania, S., Singh, S., Ploder, L., Ganaie, S., Chen, R.E., Leung, D.W., Pandolfi, P.P., Novelli, G., Matusali, G., Colavita, F., Capobianchi, M.R., Jain, S., Gupta, J.B., Amarasinghe, G.K., Diamond, M.S., Rini, J., Sidhu, S.S.
      (2020) Biorxiv --: --
    Organizational Affiliation: 

    The Donnelly Centre, University of Toronto, Toronto, Canada. Electronic address: sachdev.sidhu@utoronto.ca.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fab 15033 heavy chainA [auth H],
C [auth I]		225Homo sapiensMutation(s): 0 
Gene Names: IgH
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fab 15033 light chainB [auth L],
D [auth M]		214Homo sapiensMutation(s): 0 
Gene Names: IGK
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoproteinE [auth B],
F [auth A]		201Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
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UniProt GroupP0DTC2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
G [auth B],
H [auth A]		2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.272 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 197.1α = 90
b = 197.1β = 90
c = 211.51γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-10
    Type: Initial release
  • Version 1.1: 2021-08-18
    Changes: Database references
  • Version 1.2: 2021-08-25
    Changes: Database references